Skip to content

E-File Form 941 in QuickBooks Desktop

E-File Form 941 in QuickBooks Desktop

To electronically file form 941 on QuickBooks desktop, you need to have an active payroll subscription. Then you have to set up online tax filing and payment in the service that you purchased. While the assisted version comes already set up because Intuit does the tax filing for you, the enhanced version requires you to set up a federal e-file and e-pay. As filing tax forms on time is an essential task, you need to do it regularly and accurately to comply with the law. QuickBooks payroll enhanced enables you to quickly and easily file tax forms such as 941/944 and 941. When you’ve filed the tax form, you can make online payments as well. 

What is Form 941?

Unlike individuals, who file taxes yearly, businesses with employees must file quarterly federal tax returns to report federal withholdings from employees.

Form 941 is used to:

  • Report withholdings from employee’s paychecks for:
    • Income taxes
    • Social security tax
    • Medicare tax
  • Pay the employer’s contribution for:
    • Social security tax
    • Medicare tax

Information required on the tax Form 941 includes:

  • Total number of employees
  • Total wages paid to the employees
  • Federal tax withheld from employees
  • Social security withholdings
  • Medicare withholdings
  • Adjustments

Quarterly deadline for Form 941: 

  • April 30
  • July 31
  • October 31
  • January 31

Penalty for failure to file Form 941: 5-25 percent of tax due with the particular tax return.

Set up Federal taxes payment in QuickBooks Desktop

Before you even begin filing and paying taxes online, you have to set up the feature in the QuickBooks desktop so that you can use the feature and work with it. An organization has to enroll in the Electronic Federal Tax Payment system only once.

You can reach out to the IRS to find if you’re already enrolled in the EFTPS.

If your businesses started before 2011, then you need to follow these steps:

  1. Visit
  2. Choose the Enrollment tab.
  3. Follow on-screen instruction and input the required information to enroll your business into the Electronic Federal Tax Payment system.
  4. Wait for up to 10 business days to receive the EFTPS PIN.
  5. Go back to website.
  6. From the Login tab, log into your account and provide the necessary information to create a password.

After creating the PIN and enrollment number, you can use the Direct Deposit method to pay your employees and use the e-filing and payment systems.

Now you have to set up your tax payments. Follows these steps for the same:

  1. From the Employees menu, choose the Payroll Taxes & liabilities. 
  2. Go to Edit Payment Due Dates/Methods.
  3. Click on Schedule Payments.
  4. Choose Federal 941/944/943.
  5. When the Edit Payment Schedule window appears, click on the payment method E-pay. This enables the electronic payment of the tax form 941.
  6. Choose the frequency of payments – the number of months after which you want to file and pay the form 941.
  7. Choose the E-pay accounts to complete the electronic payment of form 941. 
  8. Provide the details of the bank account, then choose Finish.

Now you’ve set up electronic payment for Form 941. Beyond this, you have to go to QuickBooks and set up the electronic filing of taxes. Once you file the tax, you can make the payment using the information that you provided to register for electronic federal taxes payment.

Set up an e-file of federal taxes in QuickBooks

After setting up the payment system, you can go ahead with setting up federal tax filing in QuickBooks payroll. This will enable you to file the taxes, then make the payment online. While you’ve to set up the payment from the website, you can set up the tax filing process in QuickBooks payroll itesle.

Here’s the method to set up federal tax-form filing online:

  1. From the Employee menu, click on payroll tax Forms & W-2s.
  2. Choose the Process Payroll Forms.
  3. Clock on the Other Activities list.
  4. Click on Manage Filing Methods.
  5. Choose the Filing Methods option.
  6. Click on Edit.
  7. Click on Filing as Responsible Individual (Owner/Partner/Corporate Officer) for a single FEIN from the “Select how you want to file the Form…” option.
  8. Choose the E-file option, then Finish option.

Once you’ve done this step, you now have to enroll in the e-file program, which is offered by the IRS. Enrolling in this program enables you to file federal taxes online directly from QuickBooks. You’ll have to provide information such as your company’s EIN number, legal name and address.

Here are the steps to enroll in the IRS e-file program:

  1. From the Filing Methods window, choose the Enrollments option.
  2. Click on IRS, then choose Edit.
  3. Follow the on-screen instructions, then enter all the required information such as:
    1. EIN number
    2. Name of business
    3. Address of business
  4. Now enter more information for the contact person for your business. The IRS will reach out to this person for any information related to your tax filing and payment.
  5. Click on Next.
  6. Choose Send Information.

The person whose information you provide to the IRS must be a member of your organization and not a third party accountant. If the person isn’t associated directly with your company, then you shouldn’t provide his or her information for contact. Instead choose an active member of your organization.

After the IRS verifies your information, you’ll receive a confirmation in the QuickBooks Desktop payroll service. The status of the enroll will show as Accepted. You’ll also receive the 10-digit EIN number by mail on the address that you provided for contact.

Filing and paying the form 941 tax in QuickBooks Desktop

After you’ve set up the electronic tax filing and payment in QuickBooks payroll desktop, you can move forward with actually filing and paying tax form 941 in QuickBooks. You need to pay and file your 941 taxes each year – either manually or electronically. The best way to ensure compliance and regularly pay your taxes is to use QuickBooks payroll and set up a schedule.

Steps to e-file your federal tax form 941 with QuickBooks desktop:

  1. Choose the Employees option.
  2. Click on Payroll Tax Forms and W-2s.
  3. Choose Process Payroll Forms.
  4. Choose the Form 941 or another federal form that you want to file.
  5. Click on Create Form, then choose the financial period for which you want to file the form. Choose Ok.
  6. Review the form and input the required information. 
  7. Click on Check for errors to find any inaccuracies and make the required corrections.
  8. Click on Submit Form, then E-file.
  9. Input the 10-digit E-file PIN that you created when setting up e-filing with the IRS.

After you file the 941 tax through QuickBooks, you’ll receive a confirmation email within 48 hours. 

If you want to make the electronic payment for the 941 federal tax form, you can follow the steps given below:

  1. From the Employees menu, click on the Payroll Center option.
  2. Go to the Pay Liabilities tab, then choose the View/Pay button from the section titled Pay Taxes & Other Liabilities.
  3. Go through all the information to ensure accuracy, then choose E-pay.
  4. Input the 4-digit EFTPS PIN that you received when you registered for the electronic federal tax payment system. In case you have changed the bank account for the electronic payment of federal taxes, then input the latest PIN.
  5. Choose Submit.
  6. Click on Print if you want a confirmation notice of the tax payment. Then choose Close.

You can skip the step to print the confirmation of the tax payment. You’ll generally receive a confirmation mail on the registered email address. But you can go on further to check the status of your tax filing or payment. By confirming properly, you can easily ensure that you’ve filed and paid your taxes without any problems or errors.

Check the status of electronic filing and payment of the 941 tax form

To make sure that you’ve filed and paid the 941 tax on time, you can check the status of the tax online. To check the status of the 941 tax, you need the following:

  • An active subscription of QuickBooks Desktop Payroll Enhanced or Assisted.
  • An active internet connection.

Note: it may take the IRS up to 48 hours to process the electronic filing or payment of your 941 tax. So if the status doesn’t display as filed or paid, then you can wait for the first 48 hours to finish before you contact the IRS to enquire about the same. In many cases, the IRS processes the form and payment within the first 24 hours.

Steps to check for the electronic payment status of tax form 941 in QuickBooks desktop:

  1. Click on the Employees option from the main menu.
  2. Choose the Payroll Center.
  3. Go to the Pay Liabilities tab.
  4. Go to the E-payments tab from the section titled Payment History.
  5. From the Audit Trail column, click on the View option for more details about the payment status of your form 941.

Steps to check for the electronic filing status of tax form 941:

  1. From the Employees menu, click on the Payroll Center.
  2. Click on the File Forms tab, then choose the E-filing tab from the section titled Filing History.
  3. From the Audit Trail column, click on the View link option.

QuickBooks will give you the current status of your electronic filing or payment of tax 941. Because there are multiple statu messages available, you may need a little more context to understand the whole thing.

Here’s what the status message for electronic filing or payment of tax form 941 means:

  • Submitted to Intuit: you’ve filed or submitted the tax form to Intuit, which will take the next steps to ensure that you comply with the law.
  • Intuit rejected: When there’s a problem in the information you provided or a problem with the payment, Intuit will reject the filing or payment respectively. In rare cases, Intuit may reject the form submission or payment because of server connection issues.
  • Submitted to the agency: if Intuit has submitted the payment or tax form to the IRS or the appropriate state tax agency, then you’ll receive this status.
  • Agency rejected: if the IRS or the state tax agency that received the form or payment rejected it, then you’ll receive this status message – with a solution in many cases.
  • Agency accepted: this means that your filing or payment for form 941 was successful.

In most cases, your e-filing or e-payment is accepted by both the IRS and the tax agency. However, if there is any problem due to which your payment or tax filing has been rejected at any point, then you’ll receive more information about the same along with possible solutions.


I hope that I was able to help you electronically file form 941 directly from QuickBooks desktop. After you set up electronic payment or filing of form 941, you may have to wait a few days for the approval and to receive the EIN number. After that, you can go ahead with filling the tax form 941 and paying the tax amount online.


Q. When I open QuickBooks, it prompts me to “Check E-payment status”. What should I do now?

This may happen when you’re trying to make an electronic payment but the status of the prior electronic payments hasn’t been updated yet. Updating the status of all your e-payments is necessary so that your records match with those of Intuit. Here’s how you can update the status of your e-payments when filing form 941 online:

  1. From the Employees menu, choose Payroll Center.
  2. Click on the Pay Liabilities tab, then choose the E-payments tab from the section titled payment history.
  3. Click on Refresh against the payment that is causing the check status message to appear.

Q. Do I get a confirmation email after the agency accepts my payment or tax form 941 submission?

Yes, you do. When the agency accepts or rejects your electronic payment or tax filing, you’ll receive an email on the registered email address. You can then take further steps to ensure that you’ve complied with the law and followed the instructions properly.

Q. I’m getting the error message “Problem: Your email address is invalid or missing”. How do I fix it?

A. This error implies that the email address provided in company preferences isn’t correct. So the user has to take the necessary steps to add the correct email address by following these steps:

  1. From the Company menu, click on My Company.
  2. Choose the Edit icon besides the company information.
  3. Go to the Email field and make the necessary corrections or add another email address.
  4. Click on Ok to save the changes.

Now you can go back and check the history of electronic tax payment and filing without encountering the error “your email address is invalid or incorrect.”

Speak to A Specialist about QuickBooks Software

Headache🥺. Huh, Save time & money with QuickBooks Support 24×7 @ +1/, we provide assistance to those who face problems while using QuickBooks (Support all U.S. & Canada Editions)

--- Support - We provide solutions for the following QuickBooks (Pro, Premier, Accountant, Enterprise, Payroll, Cloud) ---

  • Error Support
  • Data Import
  • Data Conversion
  • Payment Solutions
  • Upgradation
  • Payroll Support
  • Data Export
  • Software Integration
  • QuickBooks Printer Support
  • Complete QuickBooks Solutions
  • Tax-Related Issues
  • Data Damage Recovery
  • Installation, Activation Help
  • QuickBooks Windows Support

Disclaimer : We are a third party agency working on providing authentic support and full fledged services for for accounting software QuickBooks 2018 version. It is one of… Read more